Bork Group

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Published May 3, 2021 | Version v1.0.2
Software Open

GUNC: detection of chimerism and contamination in prokaryotic genomes.

Creators

  • 1. Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
  • 2. Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, China
  • 3. Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
  • 4. Department of Medical Microbiology, Amsterdam University Medical Center, Amsterdam, The Netherlands
  • 5. Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.; Max Delbrück Centre for Molecular Medicine, Berlin, Germany.; Yonsei Frontier Lab (YFL), Yonsei University, Seoul 03722, South Korea.; Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.

Description

v1.0.2 Features

  • GUNC can now be run with GTDB database
  • Added option to download GTDB_GUNC database
  • Input file options can be gene_calls (faa) instead of fna if --gene_calls flag is set
  • Input genecalls can be gzipped
  • Output maxCSS file is now sorted

Bugfixes

  • Fix version of dependancy: requests>=2.22.0 (older versions not compatable)
  • Better error message if gunc_db does not exist
  • checkm_merge didnt work with unless checkm qa was run with -o 2

Other

  • Documentation updates
    • Links to synthetic datasets added
    • Citations for diamond and prodigal added
    • Clarified how checkM should be run for checkm_merge
    • Corrected command for download_db
  • Check if fasta is given with -f option instead of list of filepaths

Files

grp-bork/gunc-v1.0.2.zip

Files (2.1 MB)

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md5:8677cf54d44368266595cc246ed1d801
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Additional details

Related works

Is supplement to
https://github.com/grp-bork/gunc/tree/v1.0.2 (URL)